Volume 20, Issue 11, Pages 1929-1939 (November 2012) The Survival Motor Neuron Protein Forms Soluble Glycine Zipper Oligomers  Renee Martin, Kushol Gupta, Nisha S. Ninan, Kay Perry, Gregory D. Van Duyne  Structure  Volume 20, Issue 11, Pages 1929-1939 (November 2012) DOI: 10.1016/j.str.2012.08.024 Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 1 Conserved Regions of the SMN Protein (A) Domain structure of SMN. The conserved Gemin2-binding, Tudor, and YG-box domains are indicated. Asterisks indicate the approximate locations of amino acid changes resulting from reported SMA patient mutations. (B) Alignment of SMN YG-box sequences from diverse organisms. Residues identical in four out of the six sequences are in boldface type. The S, Y, and G repeat motifs are indicated. Hs, human; Mm, mouse; Dr, zebrafish; Ce, worm; Dm, fly; Sp, fission yeast. Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 2 Oligomerization of the SMNΔ5-Gemin2 Complex (A) Size-exclusion chromatography (SEC) of SMNΔ-Gemin2, coupled with in-line multi-angle light scattering detection (SEC-MALS). The weight-averaged molecular weight (Mw) of the majority of SMN complex ranges from 100–300 kDa. The elution position of the 670 kDa thyroglobulin marker is indicated for reference. (B) Sedimentation equilibrium carried out at four rotor speeds and two complex concentrations (3.0 and 4.3 μM) at 4°C. Radial absorbances for the 4.3 μM concentration are shown. The data cannot be fit well to a single species. The fit shown is for a dimer-tetramer-octamer equilibrium, with K4–8 = 3 μM and K2–4 = 0.4 μM. Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 3 The MBP-YG-Box Model System (A) Schematic of MPB-YG-box fusions. Tightly coupled fusions with a small number of SMN residues between the MBP C terminus and the conserved region of the YG-box are restricted to be monomers or dimers. Longer linkers allow higher oligomerization states. (B) SEC-MALS of MBP-YG252–294 (dark curve) and MBP-YGΔ7252–282 (light curve). The wild-type YG-box (46 kDa) forms stable tetramers (experimental Mw = 183 kDa) but the corresponding construct containing the sequence from SMNΔ7 is monomeric (Mw = 42 kDa). Mw is the average weight-averaged molecular weight across the center of the peak. (C) Sedimentation equilibrium of MBP-YG252–294 carried out at two concentrations (6.3 and 12.6 μM) and four rotor speeds (the 6.3 μM concentration is shown). The fit shown is for a single species tetramer model with molecular weight = 190 kDa. See also Figure S1 and Table S1. Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 4 Structure of the SMN YG-Box (A) Electron density of the SMN YG-box, near the center of the conserved region. A weighted, 1.9 Å resolution 2Fo-Fc map contoured at 1.4σ is shown. (B) Structure of the SMN YG-box dimer. The dimer is right-handed, with a −34° interhelical dihedral angle. Conserved tyrosine side chains in the YxxxYxxxY motif (Y268, Y272, and Y276) pack against conserved i+3 glycine backbone atoms in the GxxxGxxxG motif (G271, G275, and G279). The α-carbon atoms of these glycine residues are drawn as a spheres. Oligomeric states of the MBP-YG252–294 constructs with single alanine substitutions were determined by SEC-MALS analysis and are indicated in parentheses. t, primarily tetramer; m, primarily monomer; e, significant monomer and tetramer; t∗, higher order oligomers in the 200–350 kDa range are also present; e∗, monomer, dimer, and tetramer species present. (C) Structure of the MBP-YG-box dimer. The SMN YG-box forms a continuous helix with the C-terminal helix of MBP (colored). The inter-subunit contacts in the dimer are almost exclusively between YG-box helices. There are no MBP-MBP interactions and few MBP-YG-box interactions. See also Figure S2. Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 5 Tyrosine-Glycine Interactions in the YG-Zipper Dimer A stereo view of the dimer interface in the region including the Tyr268-Gly271 and Tyr272-Gly275 pairs is shown. Note the intimate Gly271-Gly271 and Gly275-Gly275 packing between helices. Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 6 Glycine Zipper Oligomers The SMN YG-box dimer is shown for comparison in (A). Examples of higher order glycine zipper oligomer structures are (B) the pore-forming helices from the KcsA potassium channel tetramer (PDB 1BL8), (C) mechanosensitive channel MscL pentamer (PDB 1MSL), and (D) mechanosensitive channel MscS heptamer (PDB 1MXM). Conserved glycine Cα atoms are drawn as red spheres and for (A), the conserved tyrosine side chains are drawn as sticks. See also Figure S3. Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 7 Oligomerization of MBP-YG Mutants (A) Effects of alanine substitution of residues from Gly261-Asn283 on oligomerization of MBP-YG252–294. These results are also indicated in Figure 4B. (B) Oligomeric states of C-terminal truncations of MBP-YG252–294. (C) Oligomeric states of exon 7 substitutions and deletions, using the MBP-YG252–294 construct. Oligomeric states were determined from SEC-MALS analysis of purified fusion proteins and are defined as in Figure 4B (a, high molecular weight aggregates). Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 8 Effects of SMA Patient Mutations on Oligomerization The results of SEC-MALS analyses of SMA patient substitutions using the MBP-YG252–294 construct, mapped onto the YG-box dimer structure. Defective and intermediate oligomerization properties are colored blue and gray, respectively. Structure 2012 20, 1929-1939DOI: (10.1016/j.str.2012.08.024) Copyright © 2012 Elsevier Ltd Terms and Conditions